5OMV

Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site

PDB DOI: https://doi.org/10.2210/pdb5OMV/pdb
NAKB: 5OMV

Classification: TRANSFERASE
Organism(s): Thermococcus sp. 9oN-7, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-08-01 Released: 2017-12-20
Deposition Author(s): Betz, K., Marx, A., Diederichs, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.189
R-Value Observed: 0.192

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of ternary complexes of archaeal B-family DNA polymerases.

Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.

(2017) PLoS One 12: e0188005-e0188005

PubMed: 29211756 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0188005
Primary Citation of Related Structures:
5OMF, 5OMQ, 5OMV

PubMed Abstract:
Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.

Organizational Affiliation

Konstanz Research School Chemical Biology, University of Konstanz, Baden-Württemberg, Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 99.36 kDa
Atom Count: 7,007
Modelled Residue Count: 785
Deposited Residue Count: 803
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	775	Thermococcus sp. 9oN-7	Mutation(s): 2 Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7)) Explore Q56366 Go to UniProtKB: Q56366
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q56366
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA template	B [auth T]	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA primer	C [auth P]	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP (Subject of Investigation/LOI) Query on DTP Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth T] MOL2 format, chain F [auth A] MOL2 format, chain J [auth T] mmCIF format, chain F [auth A] mmCIF format, chain J [auth T]	F [auth A], J [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth T] Interactions & Density Focus chain F [auth A] Focus chain J [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233
R-Value Work: 0.189
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.688	α = 90
b = 94.964	β = 90
c = 158.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Betz, K.

Marx, A.

Diederichs, K.

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2018-09-12
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description